Abstract Background Infection with carbapenem-resistant Acinetobacter baumannii has been associated with high morbidity and mortality in solid organ transplant recipients. The main objective of this study was to assess the influence of carbapenem resistance and other potential risk factors on the outcome of A. baumannii infection after kidney and liver transplantation. Methods Retrospective study of a case series of A. baumannii infection among liver and renal transplant recipients. The primary outcome was death associated with A. baumannii infection. Multivariate logistic regression was used to assess the influence of carbapenem resistance and other covariates on the outcome. Results Forty-nine cases of A. baumannii infection affecting 24 kidney and 25 liver transplant recipients were studied. Eighteen cases (37%) were caused by carbapenem-resistant isolates. There were 17 (35%) deaths associated with A. baumannii infection. In unadjusted analysis, liver transplantation (p = 0.003), acquisition in intensive care unit (p = 0.001), extra-urinary site of infection (p < 0.001), mechanical ventilation (p = 0.001), use of central venous catheter (p = 0.008) and presentation with septic shock (p = 0.02) were significantly related to a higher risk of mortality associated with A. baumannii infection. The number of deaths associated with A. baumannii infection was higher among patients infected with carbapenem-resistant isolates, but the difference was not significant (p = 0.28). In multivariate analysis, the risk of A. baumannii-associated mortality was higher in patients with infection acquired in the intensive care unit (odds ratio [OR] = 34.8, p = 0.01) and on mechanical ventilation (OR = 15.2, p = 0.04). Appropriate empiric antimicrobial therapy was associated with significantly lower mortality (OR = 0.04, p = 0.03), but carbapenem resistance had no impact on it (OR = 0.73, p = 0.70). Conclusion These findings suggest that A. baumannii-associated mortality among liver and kidney transplant recipients is influenced by baseline clinical severity and by the early start of appropriate therapy, but not by carbapenem resistance.